While numerous antiviral drugs have been developed and approved for treating HIV patients, none of them eliminates HIV completely from the patients. Rather, these antiviral drugs suppress HIV replication in the patients, and are often used in combination to achieve best therapeutic effects in patients. Highly-Active Antiretroviral Therapy (HAART) is a combination therapy capable of suppressing HIV viral replication below the limit of detection in many patients. The rapid rebound of viremia following treatment interruption indicates that HAART is unable to eradicate the virus. Low levels of viremia have also been detected in many patients using ultrasensitive viral load assays with sensitivity down to 1 virion per ml plasma. It is accepted that low-level viremia persists during effective suppression by HAART; it is unclear whether this viremia derives primarily from the activation of stable viral reservoirs such as the latently infected memory-phenotype CD4+ T cells, or ongoing rounds of successful infection of active CD4+ T cells, or a combination of the two. Furthermore, some evidence exists for continued replication of the virus in cryptic reservoirs despite suppression below the standard limit of detection. This may be due to tissue-dependent distribution and efficacy of the antiviral agents.
Understanding the origin of cryptic and residual viremia under suppressed conditions is important for a number of reasons. HIV mutations arise primarily during the process of reverse transcription during the de novo infection of active CD4+ T cells. If the viremia is driven primarily by the de novo infection of active CD4+ T cells, it represents an ongoing source of viral mutants that could eventually result in mutational escape from antiviral therapy. The activation of reservoir cells, which does not involve a new round of reverse transcription, does not result in the production of new viral mutants, and cannot by itself drive the evolution of antiviral resistance.
Genotypic studies of the residual plasma viremia have shown little or no development of new resistance mutations, which has been interpreted as evidence that residual viremia is primarily the result of activation of quiescent reservoirs. Recent analysis of HIV envelope proteins in the gut-associated lymphoid tissue (GALT) has likewise shown no evidence of evolution during suppressive therapy. Treatment intensification has consistently shown no significant decrease in the residual plasma viremia. Conversely, a genotypic study focused on episomal cDNA collected prior to viral rebound indicated that the episomal cDNA showed evidence of recent evolution, implying de novo replication as the source.
Many authors have suggested using episomal artifacts of HIV infection as surrogate markers of replication, including linear unintegrated DNA, 1-LTR, and 2-LTR circular DNA. 2-LTR artifacts are especially useful as the 2-LTR region of the genome is unique to the episomal artifact as compared to linear integrated DNA. However, the use of 2-LTR as a surrogate marker is controversial, primarily due to controversy regarding the half-life of the episomes. 2-LTR circles have been shown to be stable in vitro, leading to the conclusion that they are not an effective surrogate measurement of recent infection. Studies estimating the half-life of the circles in vivo, however, indicate that they are highly labile, with half-lives of only a few days. One possible explanation is that the host cells may have significantly shorter half-lives in vivo than in vitro, possibly due to a high likelihood of programmed proliferation in 2-LTR-containing cells.
There remains a need for reliable methods to detect cryptic viremia in patients receiving a suppressive antiviral therapy for assessing or predicting the efficacy of the suppressive antiviral therapy.